Article
Computer Science, Theory & Methods
Zar Bakht Imtiaz, Awais Manzoor, Saif ul Islam, Malik Ali Judge, Kim-Kwang Raymond Choo, Joel J. P. C. Rodrigues
Summary: Discovering communities is important in complex networks, and community detection is an optimization problem. The proposed MLACO algorithm, using RC and KKM as objective functions, outperforms other methods, demonstrating its utility.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Article
Management
Kyungduk Moon, Kangbok Lee, Sunil Chopra, Steve Kwon
Summary: This paper studies a logical inference problem in Boolean networks and proposes a bilevel integer programming model and a branch and bound algorithm to find critical genetic alterations in a minimal way. Computational experiments show the effectiveness of the algorithm.
EUROPEAN JOURNAL OF OPERATIONAL RESEARCH
(2022)
Article
Computer Science, Artificial Intelligence
Moises Silva-Munoz, Carlos Contreras-Bolton, Carlos Rey, Victor Parada
Summary: One of the fundamental problems in graph optimization is determining the maximum set of unconnected vertices, known as the maximum independent set problem. This paper presents a new artificially generated algorithm for solving this problem. The algorithm is generated using genetic programming, combining heuristics, a tabu search method, and an exact mathematical formulation to find the best computational performance among all generated algorithms.
APPLIED SOFT COMPUTING
(2023)
Article
Construction & Building Technology
Alireza Akbari-Dibavar, Amir Farahmand-Zahed, Behnam Mohammadi-Ivatloo, Kazem Zare
Summary: This paper addresses the inefficient dispatch of multiple-chiller systems by establishing a hybrid algorithm to solve the optimal chiller loading problem, with results showing its effectiveness and superiority through comparison analysis.
ENERGY AND BUILDINGS
(2022)
Article
Computer Science, Interdisciplinary Applications
Xudong Wang, Zeyu Liu, Xueping Li
Summary: The past decade has seen the rapid growth of drone-assisted delivery in e-commerce companies. This study extends the classic vehicle routing problem by optimally scheduling operations in a package depot center using a fleet of drones with different capacities, speeds, and maximum flight ranges. The problem is formulated as a mixed integer programming model and solved using FIFO-based and rescheduling-based genetic algorithms. Numerical experiments show the efficiency and practicality of the proposed algorithms for real-world implementations.
COMPUTERS & INDUSTRIAL ENGINEERING
(2023)
Article
Computer Science, Artificial Intelligence
S. Ali Lajevardy, Mehrdad Kargari
Summary: Advances in molecular biology have led to an increase in genome sequencing, with sequence alignment being the first step in understanding molecular function. Multiple sequence alignment (MSA) is more advantageous than pairwise sequence alignment (PSA) as it predicts similarity in a family of similar sequences. However, the use of dynamic programming in MSA adds complexity, leading to the adoption of heuristic and approximation methods.
Article
Computer Science, Artificial Intelligence
Vincent F. Yu, Nabila Yuraisyah Salsabila, Nurhadi Siswanto, Po-Hsun Kuo
Summary: The research proposes a joint optimization model for managing spare parts inventory and planned maintenance to balance inventory cost and spare parts availability. The study shows that the independent policy results in lower cost than the aggregate policy, and the proposed Genetic Algorithm performs efficiently for large-scale problems.
APPLIED SOFT COMPUTING
(2022)
Article
Computer Science, Interdisciplinary Applications
Wisute Ongcunaruk, Pornthipa Ongkunaruk, Gerrit K. Janssens
Summary: This study aims to improve transportation planning decisions for a production company in Thailand through a mixed integer programming model and a genetic algorithm, resulting in reduced costs and increased efficiency.
COMPUTERS & INDUSTRIAL ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Tomas Thorbjarnarson, Neil Yorke-Smith
Summary: Recent research has shown potential in optimizing certain aspects of neural networks (NNs) using Mixed Integer Programming (MIP) solvers. However, the approach of training NNs with MIP solvers has not been explored thoroughly. This article introduces new MIP models for training integer-valued neural networks (INNs) and provides two methods to improve the efficiency and data handling capabilities of MIP solvers. Experimental results demonstrate the superiority of our approach in terms of accuracy, training time, and data usage compared to previous state-of-the-art methods. Our methodology is particularly proficient at training NNs with minimal data and memory requirements, making it valuable for deployment on low-memory devices.
Article
Physics, Fluids & Plasmas
Lukasz G. Gajewski, Julian Sienkiewicz, Janusz A. Holyst
Summary: By analyzing the frequency spectrum of wave dynamics, researchers can uncover hidden multilayer structures in complex networks and successfully extract the number of unknown layers involved. They demonstrate that with a sufficient observation time, the full reconstruction of the adjacency matrix spectrum is possible, aiding in understanding the structure of multilayer systems.
Article
Engineering, Chemical
Jun Yang, Tong Sun, Xiuxiang Huang, Ke Peng, Zhongxiang Chen, Guoguang Qian, Zekai Qian
Summary: This paper presents a solution method for a large-scale automotive parts paint shop scheduling problem, incorporating color arrangement, part arrangement, bracket restrictions, and multi-objectives. By converting the multi-objective model into a multi-level objective programming problem and utilizing rule-based algorithm and adaptive genetic algorithm, the problem was successfully solved.
Article
Computer Science, Cybernetics
Ling He, Wenzhong Guo, Yuzhong Chen, Kun Guo, Qifeng Zhuang
Summary: In this article, an incremental clustering algorithm for discovering overlapping communities in dynamic networks is proposed, using a degree-based seed selection strategy and a four-staged framework based on cascade information diffusion for community updates. Experiments demonstrate that the algorithm effectively discovers overlapping communities in dynamic networks and outperforms existing algorithms.
IEEE TRANSACTIONS ON COMPUTATIONAL SOCIAL SYSTEMS
(2022)
Article
Computer Science, Theory & Methods
Mohammad K. Fallah, Mahmood Fazlali, Masoud Daneshtalab
Summary: This paper introduces a parallel genetic algorithm based on LP Relaxation, which solves large-scale ILP models through incremental learning technique and achieves better performance than previous algorithms.
Article
Engineering, Multidisciplinary
Byoungwook Kim, Hong-Jun Jang
Summary: This paper introduces a new algorithm, Genetic algorithm-based Keyword Matching DBSCAN (GKM-DBSCAN), to discover adjacent clusters among the cluster results of the keyword-based DBSCAN algorithm. Experimental results show that GKM-DBSCAN outperforms the brute-force method by up to 21 times.
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES
(2023)
Article
Chemistry, Analytical
Andrzej Bozek
Summary: Stick-slip is a negative phenomenon caused by friction in servo systems. Existing control algorithms have been studied to suppress stick-slip, but no simple solution has been found. In this study, a new approach based on genetic programming was proposed to discover an optimal servo control algorithm for suppressing stick-slip. The results show that genetic programming can successfully discover an effective control algorithm.
Article
Biochemistry & Molecular Biology
Melina M. Musri, Nuria Coll-Bonfill, Bradley A. Maron, Victor I. Peinado, Rui-Sheng Wang, Jordi Altirriba, Isabel Blanco, William M. Oldham, Olga Tura-Ceide, Jessica Garcia-Lucio, Benjamin de la Cruz-Thea, Gunter Meister, Joseph Loscalzo, Joan A. Barbera
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2018)
Review
Biochemistry & Molecular Biology
Wusheng Xiao, Rui-Sheng Wang, Diane E. Handy, Joseph Loscalzo
ANTIOXIDANTS & REDOX SIGNALING
(2018)
Article
Cardiac & Cardiovascular Systems
William M. Oldham, Rudolf K. F. Oliveira, Rui-Sheng Wang, Alexander R. Opotowsky, David M. Rubins, Jon Hainer, Bradley M. Wertheim, George A. Alba, Gaurav Choudhary, Adrienn Tornyos, Calum A. MacRae, Joseph Loscalzo, Jane A. Leopold, Aaron B. Waxman, Horst Olschewski, Gabor Kovacs, David M. Systrom, Bradley A. Maron
CIRCULATION RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Rui-Sheng Wang, Joseph Loscalzo
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Cell Biology
Andriy O. Samokhin, Thomas Stephens, Bradley M. Wertheim, Rui-Sheng Wang, Sara O. Vargas, Lai-Ming Yung, Minwei Cao, Marcel Brown, Elena Arons, Paul B. Dieffenbach, Jason G. Fewell, Majed Matar, Frederick P. Bowman, Kathleen J. Haley, George A. Alba, Stefano M. Marino, Rahul Kumar, Ivan O. Rosas, Aaron B. Waxman, William M. Oldham, Dinesh Khanna, Brian B. Graham, Sachiko Seo, Vadim N. Gladyshev, Paul B. Yu, Laura E. Fredenburgh, Joseph Loscalzo, Jane A. Leopold, Bradley A. Maron
SCIENCE TRANSLATIONAL MEDICINE
(2018)
Article
Multidisciplinary Sciences
Feixiong Cheng, Rishi J. Desai, Diane E. Handy, Ruisheng Wang, Sebastian Schneeweiss, Albert-Laszlo Barabasi, Joseph Loscalzo
NATURE COMMUNICATIONS
(2018)
Review
Biochemistry & Molecular Biology
Rui-Sheng Wang, William M. Oldham, Bradley A. Maron, Joseph Loscalzo
ANTIOXIDANTS & REDOX SIGNALING
(2018)
Article
Critical Care Medicine
Maria G. Frid, B. Alexandre McKeon, Joshua M. Thurman, Bradley A. Maron, Min Li, Hui Zhang, Sushil Kumar, Timothy Sullivan, Jennifer Laskowsky, Mehdi A. Fini, Samantha Hu, Rubin M. Tuder, Aneta Gandjeva, Martin R. Wilkins, Christopher J. Rhodes, Pavandeep Ghataorhe, Jane A. Leopold, Rui-Sheng Wang, V. Michael Holers, Kurt R. Stenmark
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2020)
Article
Pharmacology & Pharmacy
Rui-Sheng Wang, Damien C. Croteau-Chonka, Edwin K. Silverman, J. Loscalzo, Scott T. Weiss, Kathryn T. Hall
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2019)
Article
Multidisciplinary Sciences
Feixiong Cheng, Weiqiang Lu, Chuang Liu, Jiansong Fang, Yuan Hou, Diane E. Handy, Ruisheng Wang, Yuzheng Zhao, Yi Yang, Jin Huang, David E. Hill, Marc Vidal, Charis Eng, Joseph Loscalzo
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Euijun Song, Rui-Sheng Wang, Jane A. Leopold, Joseph Loscalzo
Article
Pharmacology & Pharmacy
Rui-Sheng Wang, Joseph Loscalzo
Summary: PAH is a serious cardiopulmonary disease that significantly impacts patient lifespan and quality of life, with a poor long-term prognosis and survival rate despite medical advancements. A network module-based approach is used in this study to identify potential drug repositioning candidates for treating PAH, helping to gain mechanistic insights into how these drugs can target the underlying pathobiological mechanisms. This study identified 53 drugs that could potentially be repurposed for PAH treatment, providing new avenues for drug development in this challenging disease.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Rui-Sheng Wang, Joseph Loscalzo
Summary: There may be common pathobiological processes between COVID-19 and PAH, which is important for discovering therapeutic targets and designing personalized treatments for COVID-19 patients with PAH.
PULMONARY CIRCULATION
(2023)
Article
Pharmacology & Pharmacy
Julian Spaeth, Rui-Sheng Wang, Maeve Humphrey, Jan Baumbach, Joseph Loscalzo
Summary: This study presents a machine learning framework that integrates various target network features and physicochemical properties of compounds to analyze their influence on the therapeutic effects for SARS-CoV-2 infection and host cell cytotoxic effects. The models achieve a reasonable mean area under the receiver operating characteristic curve (ROC-AUC) of 0.73 on an unseen validation set, providing insights into the determinants of drug efficacy and cytotoxicity.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
(2023)
Article
Medicine, Research & Experimental
Rui-Sheng Wang, Kathryn T. Hall, Franco Giulianini, Dani Passow, Ted J. Kaptchuk, Joseph Loscalzo